Abstract Background This study aimed to evaluate the clinical and functional outcomes of patients with femoral and tibial critical-sized bone defect (CSBD) treated by trifocal bone transport using the Ilizarov method. Methods From March 2011 and January 2017, clinical and radiographic data of patients with CSBD (> 6 cm) caused by infection were documented and analyzed. Patients were divided into the femur group (n = 18) and tibia groups (n = 21) according to the location of bone transport. The bone and functional outcomes were evaluated according to the Association for the Study and Application of the Method of the Ilizarov (ASAMI) criterion, and postoperative complications were evaluated by Paley classification. Results A total of 39 patients were managed by the trifocal bone transport for the femur (n = 18) or tibia (n = 21) bone defects with a mean follow-up time of 26.1 months (range 17–34 months). Eighteen femurs and 21 tibias with a mean distraction regenerate length (DRL) of 8.3 cm (range 6–13 cm) and 7.5 cm (range 6–11 cm) respectively. Infection was eradicated in all patients, and the total bone union was received in all cases (100%). Statistical difference of bone grade (excellent/good/fair/poor, 3/11/3/1 vs 2/13/4/2, P